Cis-Antisense Transcription Gives Rise to Tunable Genetic Switch Behavior: A Mathematical Modeling Approach

Abstract

Antisense transcription has been extensively recognized as a regulatory mechanism for gene expression across all kingdoms of life. Despite the broad importance and extensive experimental determination of cis-antisense transcription, relatively little is known about its role in controlling cellular switching responses. Growing evidence suggests the presence of non-coding cis-antisense RNAs that regulate gene expression via antisense interaction. Recent studies also indicate the role of transcriptional interference in regulating expression of neighboring genes due to traffic of RNA polymerases from adjacent promoter regions. Previous models investigate these mechanisms independently, however, little is understood about how cells utilize coupling of these mechanisms in advantageous ways that could also be used to design novel synthetic genetic devices. Here, we present a mathematical modeling framework for antisense transcription that combines the effects of both transcriptional interference and cis-antisense regulation. We demonstrate the tunability of transcriptional interference through various parameters, and that coupling of transcriptional interference with cis-antisense RNA interaction gives rise to hypersensitive switches in expression of both antisense genes. When implementing additional positive and negative feed-back loops from proteins encoded by these genes, the system response acquires a bistable behavior. Our model shows that combining these multiple-levels of regulation allows fine-tuning of system parameters to give rise to a highly tunable output, ranging from a simple-first order response to biologically complex higher-order response such as tunable bistable switch. We identify important parameters affecting the cellular switch response in order to provide the design principles for tunable gene expression using antisense transcription. This presents an important insight into functional role of antisense transcription and its importance towards design of synthetic biological switches.

ADAR1 promotes robust hypoxia signaling via distinct regulation of multiple HIF‐1α‐inhibiting factors

“…HIF1A‐AS2, the antisense RNA under study, represents an unique example given its overlapping yet opposite genomic orientation relative to HIF‐1A, which give rises to a convergent transcription, and also its strong and direct activation by HIF‐1A . In line with the notion that antisense transcripts can regulate their neighboring genes in cis , a hypoxia‐associated transcriptome profiling reported by Choudhry et al showed that the expression of the sense–antisense gene pair exhibits a converse pattern under low oxygen stress—HIF1A‐AS2 is expectedly induced whereas HIF‐1A mRNA is reduced. This is consistent with our gene expression analysis (Fig A) and, together with our functional characterization of HIF1A‐AS2, strongly supportive of a transcription‐based negative‐feedback regulation.…”

Transcription-dependent DNA methylation at the imprintedZrsr1-DMR

“…A decrease in maternal expression of Commd1 also occurred concomitantly with the activation of maternal Zrsr1, which strongly suggests that the predominant maternal expression of Commd1 results from Zrsr1-mediated reduction in the expression of Commd1 from the paternal allele. Studies on genetic organization in genomes have identified overlapping and antisense-oriented genes, and the mutual cis-acting effect on their expression, which is termed transcriptional interference (Bordoy & Chatterjee, 2015). The active transcription of Zrsr1 within Commd1 may cause collisions between the opposing Zrsr1 and Commd1 elongation complexes, which would result in the reduction in their expression.…”

Engineering Transcriptional Interference through RNA Polymerase Processivity Control

“…There are two known modes of transcriptional regulation by antisense transcription: antisense RNA (asRNA) regulation, where sense and antisense RNAs hybridize to promote RNAsemediated degradation or block the ribosome binding site to prevent its translation (8)(9)(10), and collisions of the transcriptional machinery originated from sense and antisense promoters, termed transcriptional interference (TI) (8,(10)(11)(12). Three primary modes of TI-RNA Polymerase (RNAP) collisions, sitting duck, and promoter occlusion-have been proposed (11) and parsed through experiments (13) and mathematical modeling (9,14). Direct contact of bacterial RNAPs has not been observed during head-on RNAP collisions (15), and it is generally understood that interference of one RNAP on another may be mediated through DNA supercoiling (16,17) rather than due to direct collisions of transcriptional machinery.…”